Add ModelFactory for conveniently building models

ModelFactory currently compiles separately, i.e., without linkage to
the 'impl' library. This vastly reduces the amount of code in the main
function.

.gitlab-ci.yml

@@ -126,6 +126,7 @@ build:debug: &debug
       $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS dorie-rfg
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_unit_tests
+    - $DUNECONTROL --only=dorie make $MAKE_FLAGS richards_d2_r1 transport_d2_r0_t0
 
 build:debug-clang:
   <<: *debug
@@ -140,6 +141,7 @@ build:debug-clang:
       $DUNECONTROL --only=dorie configure
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS dorie-rfg
     - $DUNECONTROL --only=dorie make $MAKE_FLAGS build_unit_tests
+    - $DUNECONTROL --only=dorie make $MAKE_FLAGS transport_d2_r0_t0 transport_d2_r1_t0
 
 
 # --- Tests ---
@@ -212,7 +214,7 @@ deploy:dockerhub-devel: &deploy
     - $DOCKER_LOGIN
   script:
     - docker build -f docker/dorie.dockerfile
-      --build-arg DUNE_ENV_IMAGE=$DUNE_ENV_IMAGE --build-arg PROCNUM=$CPUS_DIND
+      --build-arg BASE_IMG_VERSION=$IMAGE_VERSION --build-arg PROCNUM=$CPUS_DIND
       -t dorie/dorie:devel .
     - docker push dorie/dorie:devel
 
@@ -222,7 +224,7 @@ deploy:dockerhub-stable:
     - tags@dorie/dorie
   script:
     - docker build -f docker/dorie.dockerfile
-      --build-arg DUNE_ENV_IMAGE=$DUNE_ENV_IMAGE --build-arg PROCNUM=$CPUS_DIND
+      --build-arg BASE_IMG_VERSION=$IMAGE_VERSION --build-arg PROCNUM=$CPUS_DIND
       -t dorie/dorie:$CI_COMMIT_TAG .
     - docker push dorie/dorie:$CI_COMMIT_TAG
 

CHANGELOG.md

@@ -43,6 +43,7 @@
 * Linear interpolator for initial conditions and scaling fields !145, !156
 * Parameterizations for hydrodynamic dispersion in solute transport !141
 * Generic Python VTK file reader !143, !150
+* Define compile-time settings via CPP macros !144
 * [Google Test](https://github.com/google/googletest) unit test framework
     as Git Submodule !159
 
@@ -151,6 +152,7 @@
 * Switch to stable `dune-randomfield` release branch !151, !153
 * System tests for executing `dorie pfg` module !153
 * Finite volume solver for the Richards equation !132
+* Build independent library and executable for each compile-time setting !144
 * `SimulationBase` unit test now uses Google Test !159
 
 ### Fixed

CMakeLists.txt

@@ -40,6 +40,10 @@ dune_project()
 dune_enable_all_packages()
 dune_require_cxx_standard(MODULE "dorie" VERSION 14)
 
+# Cache the executable path
+set(DORIE_EXE_PATH ${PROJECT_BINARY_DIR}/dune/dorie/
+    CACHE STRING "Path to the directory containing the executables")
+
 # add subdirectories
 add_subdirectory("plugins/vendor")
 add_subdirectory("m4")

cmake/modules/DorieCompileInstance.cmake

+# Default Dorie model targets
+add_custom_target("richards")
+add_custom_target("transport")
+
+# Maximum polynomial orders of Richards model for available targets
+set(DORIE_MAX_RORDER_2 6)
+set(DORIE_MAX_RORDER_3 6)
+
+# Maximum polynomial orders of transport model for available targets
+set(DORIE_MAX_TORDER_2 0)
+set(DORIE_MAX_TORDER_3 0)
+
+# Maximum polynomial orders of Richards model for default targets
+set(DORIE_MAX_DEFAULT_RORDER_2 3)
+set(DORIE_MAX_DEFAULT_RORDER_3 1)
+
+# Maximum polynomial orders of transport model for default targets
+set(DORIE_MAX_DEFAULT_TORDER_2 0)
+set(DORIE_MAX_DEFAULT_TORDER_3 0)
+
+#
+# .. cmake_function:: dorie_compile_instance
+#
+# Adds an executable and library for the specified model.
+#
+# The parameters specify static settings for the model instance. If these
+# settings comply to the limits of the default variables, the instance is
+# added to the global "richards" or "transport" targets, depending on which
+# MODEL type is built.
+#
+# In case of "transport", the appropriate "richards" library must be available.
+# Otherwise, it is also defined by this function.
+#
+# A sanity check for the input variables is not performed by CMake, but by
+# the C++ code during compile-time.
+#
+# This function takes the following arguments:
+#
+#   - MODEL: Name of the model. Accepts "richards" or "transport".
+#   - DIMENSION: Spatial dimension.
+#   - RORDER: Finite element polynomial order of the Richards module.
+#   - TORDER: Finite element polynomial order of the Transport module.
+#   - CREATED_LIB: Variable to store the created library target name in.
+#
+function(dorie_compile_instance)
+
+    # parse the function arguments
+    set(SINGLE_ARGS MODEL DIMENSION RORDER TORDER CREATED_LIB)
+    cmake_parse_arguments(ARGS "" "${SINGLE_ARGS}" "" ${ARGN})
+
+    if (ARGS_UNPARSED_ARGUMENTS)
+        message(WARNING "Unparsed arguments when calling "
+                        "'dorie_create_executable: "
+                        "${ARGS_UNPARSED_ARGUMENTS}")
+    endif ()
+
+    # set dimension string
+    set(DIM_STR "d${ARGS_DIMENSION}")
+
+    # set option string
+    set(OPTION_STR "r${ARGS_RORDER}")
+
+    # issue warning if transport order is given for 'richards'
+    if (ARGS_MODEL STREQUAL "richards")
+        set (lib_src ${PROJECT_SOURCE_DIR}/dune/dorie/model/richards/impl/impl.cc)
+        if (ARGS_TORDER)
+            message(WARNING "Ignoring argument TORDER for MODEL "
+                            "'richards'")
+        endif ()
+    # append transport order to option string
+    elseif (ARGS_MODEL STREQUAL "transport")
+        set (lib_src ${PROJECT_SOURCE_DIR}/dune/dorie/model/coupling/impl/impl.cc)
+        string(APPEND OPTION_STR "_t${ARGS_TORDER}")
+    # unknown model
+    else ()
+        message(SEND_ERROR "Unsupported model: ${ARGS_MODEL}. "
+                           "Must be either 'richards' or 'transport'")
+    endif ()
+
+    # register the library
+    set(lib_name "dorie_${ARGS_MODEL}_${DIM_STR}_${OPTION_STR}")
+    if (NOT TARGET ${lib_name})
+        add_library(${lib_name} EXCLUDE_FROM_ALL STATIC ${lib_src})
+
+        # link to dependencies
+        target_link_libraries(${lib_name}
+            PUBLIC
+                spdlog
+                muparser::muparser
+                hdf5
+                yaml-cpp
+                ${DUNE_LIBS}
+        )
+
+        # register the executable
+        set(exe_name "${ARGS_MODEL}_${DIM_STR}_${OPTION_STR}")
+        set(src_file ${CMAKE_SOURCE_DIR}/dune/dorie/${ARGS_MODEL}.cc)
+        add_executable(${exe_name} EXCLUDE_FROM_ALL ${src_file})
+        target_link_libraries(${exe_name} PUBLIC ${lib_name})
+
+        # Add the executable to the default targets
+        if ((ARGS_RORDER LESS_EQUAL DORIE_MAX_DEFAULT_RORDER_${ARGS_DIMENSION})
+            AND ((NOT ARGS_TORDER)
+                OR ARGS_TORDER LESS_EQUAL DORIE_MAX_DEFAULT_TORDER_${ARGS_DIMENSION})
+        )
+            add_dependencies(${ARGS_MODEL} ${exe_name})
+        endif()
+
+        # set compile definitions
+        target_compile_definitions(${lib_name}
+            PUBLIC
+                DORIE_DIM=${ARGS_DIMENSION}
+                DORIE_RORDER=${ARGS_RORDER})
+
+        if (ARGS_MODEL STREQUAL "transport")
+            target_compile_definitions(${lib_name}
+                PUBLIC DORIE_TORDER=${ARGS_TORDER})
+        endif ()
+    endif()
+
+    # If we build a transport model, build the Richards library as well
+    if (ARGS_MODEL STREQUAL "transport")
+        dorie_compile_instance(MODEL "richards"
+                               DIMENSION ${ARGS_DIMENSION}
+                               RORDER ${ARGS_RORDER}
+                               CREATED_LIB richards_lib
+        )
+        # ... and link to it!
+        target_link_libraries(${exe_name} PUBLIC ${richards_lib})
+    endif()
+
+    # Report the library target name
+    if (ARGS_CREATED_LIB)
+        set(${ARGS_CREATED_LIB} ${lib_name} PARENT_SCOPE)
+    endif ()
+
+endfunction()

cmake/modules/DorieMacros.cmake

+# --- DEPENDENCIES --- #
 # These macros check for the following packages, yielding the respective
 # targets
 #
@@ -47,6 +48,11 @@ message (STATUS "DUNE Libraries: ${DUNE_LIBS}")
 # Remove CMake policy stack
 cmake_policy(POP)
 
+# --- CMAKE MODULES --- #
+# Include the CMake modules used in the project
+
+include(DorieCompileInstance)
+
 # Check if testing is enabled
 if (dune-testtools_FOUND)
     message(STATUS "Testing enabled: dune-testtools found.")

doc/introduction/features.rst

@@ -82,5 +82,31 @@ the Richards solver must be utilized to solve them. Use the value
 ``richards+transport`` in the ``simulation.mode`` keyword to run the solute
 transport solver.
 
+Available Models
+================
+
+Several settings like solver coupling, spatial dimension, or polynomial order
+must be given at compile time. DORiE includes a discrete set of setting
+combinations users may choose from via the
+:doc:`configuration file </manual/config-file>`. If DORiE is run from its public
+Docker image or with the default targets built locally on your machine, these
+are the available combinations of options:
+
++----------------------+-------------------+-----------------------------+------------------------------+----------------+
+|``simulation.mode``   |``grid.dimensions``|``richards.numerics.FEorder``|``transport.numerics.FEorder``| GMSH Grid and  |
+|                      |                   |                             |                              | grid refinement|
++======================+===================+=============================+==============================+================+
+|``richards``          |  2                |  <= 3                       |   ✗                          |    ✓*          |
+|                      +-------------------+-----------------------------+------------------------------+----------------+
+|                      |  3                |  <= 1                       |   ✗                          |    ✓*          |
++----------------------+-------------------+-----------------------------+------------------------------+----------------+
+|``richards+transport``|  2                |  <= 3                       |   0                          |    ✗           |
+|                      +-------------------+-----------------------------+------------------------------+----------------+
+|                      |  3                |  <= 1                       |   0                          |    ✗           |
++----------------------+-------------------+-----------------------------+------------------------------+----------------+
+
+* *: Only for ``richards.numerics.FEorder`` > 0. Finite volume solvers do not
+  support unstructured grids.
+
 .. _DUNE: https://www.dune-project.org/
 .. _DUNE-PDELab: https://www.dune-project.org/modules/dune-pdelab/

doc/manual/initial.rst

@@ -48,7 +48,7 @@ They are controlled by the ``initial.type`` key and available for every model.
     .. tip::
        Assuming the target quantity is the matric head (see
        :ref:`initial-transformation`), typical initial conditions for a
-       Richards simulation are
+       Richards model are
 
        * Hydrostatic equilibrium: A vertical gradient of :math:`-1` and a
          fixed value ``<v>`` at height :math:`h = 0 \, \mathrm{m}`::

doc/manual/parameter-file.rst

@@ -181,10 +181,10 @@ Mualem–van Genuchten
 Transport Parameterizations
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-Regardless of the parameterization, the transport simulation always computes
+Regardless of the parameterization, the transport model always computes
 the microscopic péclet number, for which it requires the characteristic pore
 length, the molecular diffusion, and the fluid velocity. The latter is directly
-provided by the richards simulation while the other two have to be specified
+provided by the richards model while the other two have to be specified
 for each volume:
 
 Permanent parameters:
@@ -217,7 +217,7 @@ Permanent parameters:
 
 The hydrodynamic dispersion tensor :math:`\mathsf{D}_\text{hd} \,
 [\text{m}^2\text{s}^{-1}]` is the main parameter to provide in the
-transport simulation. Below you will find several parameterization for this.
+transport model. Below you will find several parameterization for this.
 
 Constant
 """"""""
@@ -358,7 +358,7 @@ Milligton-Quirk I Effective Diffusion
       D_\text{eff} = D_m \frac{\theta_w^{7/3}}{\phi^{2/3}}.
 
   where the volumetric water content :math:`\theta_w \, [-]`
-  is automatically obtained from the Richards simulation.
+  is automatically obtained from the Richards model.
 
   * ``Deff_type: Deff_MQ1``
 
@@ -389,7 +389,7 @@ Milligton-Quirk II Effective Diffusion
       D_\text{eff} = D_m \frac{\theta_w}{\phi^{2/3}}.
 
   where the volumetric water content :math:`\theta_w \, [-]`
-  is automatically obtained from the Richards simulation.
+  is automatically obtained from the Richards model.
 
   * ``Deff_type: Deff_MQ2``
 

doc/public-api.rst

@@ -21,15 +21,43 @@ The main routine (`dorie run <config>`) also requires input files for
 Code API
 ========
 
-DORiE supplies the `Simulation` template. This is the main class for assembling
-and running the solver.
+DORiE supplies the `Model` abstract base class.  All other models follow this 
+structure. 
 
-.. doxygenclass:: Dune::Dorie::RichardsSimulation
+ABC Model
+---------
+.. doxygenclass:: Dune::Dorie::ModelBase
    :members:
 
-The simulation template requires compile-time type specifications wrapped in a
+
+Model Traits
+------------
+
+The model template requires compile-time type specifications wrapped in a
 suitable `Traits` structure.
 
 .. doxygenstruct:: Dune::Dorie::BaseTraits
    :members:
    :undoc-members:
+
+Richards Model
+--------------
+
+.. doxygenclass:: Dune::Dorie::ModelRichards
+   :members:
+
+Transport Model
+---------------
+
+.. doxygenclass:: Dune::Dorie::ModelTransport
+   :members:
+
+
+Coupling Model
+--------------
+
+The coupling between Richards and Transport models is done by yet another 
+model which is in charge of managing the steps of the two sub-models.
+
+.. doxygenclass:: Dune::Dorie::ModelTransport
+   :members:
\ No newline at end of file

docker/dorie.dockerfile

-ARG DUNE_ENV_IMAGE=dorie/dune-env:2.6
-FROM $DUNE_ENV_IMAGE
+ARG BASE_IMG_VERSION=1.2
+
+# start build image
+FROM dorie/dune-env:img-v${BASE_IMG_VERSION} as build-env
+
+# maintainer info
 LABEL maintainer="lriedel@iup.uni-heidelberg.de"
+
 # number of cores for parallel builds
 ARG PROCNUM=1
 # Compilers to be used
 ARG CC=gcc
 ARG CXX=g++
 
-# build DORiE
+# copy the build context to this image
+WORKDIR /opt/dune/dorie
+COPY ./ ./
+
+# build the executable
+WORKDIR /opt/dune/
+RUN MAKE_FLAGS="-j${PROCNUM}" \
+    CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=${CC} -DCMAKE_CXX_COMPILER=${CXX} -DDUNE_PYTHON_VIRTUALENV_SETUP=True -DDUNE_PYTHON_ALLOW_GET_PIP=True" \
+    ./dune-common/bin/dunecontrol --only=dorie all
+
+# Start a fresh image as production environment
+FROM $DUNE_ENV_IMAGE as prod-env
+
+# Copy binaries, Python venv, and Python scripts (editable install)
 WORKDIR /opt/dune
-ADD . /opt/dune/dorie/
-RUN CMAKE_FLAGS="-DCMAKE_BUILD_TYPE=Release -DCMAKE_C_COMPILER=${CC} -DCMAKE_CXX_COMPILER=${CXX} -DDUNE_PYTHON_VIRTUALENV_SETUP=True -DDUNE_PYTHON_ALLOW_GET_PIP=True" \
-    ./dune-common/bin/dunecontrol --only=dorie configure \
-    && ./dune-common/bin/dunecontrol --only=dorie make -j ${PROCNUM} dorie-rfg dorie \
-    && ./dune-common/bin/dunecontrol --only=dorie exec \
-        "rm build-cmake/dune/dorie/model/richards/impl/libdorie-richards.a build-cmake/dune/dorie/model/transport/impl/libdorie-transport.a build-cmake/dune/dorie/model/richards/impl/CMakeFiles/dorie-richards.dir/*.cc.o build-cmake/dune/dorie/model/transport/impl/CMakeFiles/dorie-transport.dir/*.cc.o" 
+COPY --from=build-env /opt/dune/dune-common/build-cmake/dune-env ./dune-common/build-cmake/dune-env
+WORKDIR /opt/dune/dorie
+COPY --from=build-env /opt/dune/dorie/build-cmake ./build-cmake/
+COPY --from=build-env /opt/dune/dorie/python ./python/
 
 # move to working directory
 WORKDIR /mnt
 
 # run bash in the virtualenv (this actually creates two bash instances...)
+# TODO: create new user with restricted privileges
 ENTRYPOINT ["/opt/dune/dune-common/build-cmake/run-in-dune-env", "/bin/bash"]

dune/dorie/CMakeLists.txt

@@ -4,16 +4,23 @@ if(DORIE_TESTING)
     add_subdirectory("test")
 endif()
 
-add_executable(richards richards.cc)
-dune_target_link_libraries(richards ${DUNE_LIBS})
-target_link_libraries(richards
-    dorie-richards spdlog muparser::muparser hdf5 yaml-cpp)
 
-add_executable(transport transport.cc)
-dune_target_link_libraries(transport ${DUNE_LIBS})
-target_link_libraries(transport
-    dorie-richards dorie-transport spdlog muparser::muparser hdf5 yaml-cpp)
+# create targets for many possible combinations
+foreach(dim 2 3)
+    foreach(rorder RANGE ${DORIE_MAX_RORDER_${dim}})
+        dorie_compile_instance(MODEL "richards"
+                               DIMENSION ${dim}
+                               RORDER ${rorder})
+        foreach(torder RANGE ${DORIE_MAX_TORDER_${dim}})
+            dorie_compile_instance(MODEL "transport"
+                                   DIMENSION ${dim}
+                                   RORDER ${rorder}
+                                   TORDER ${torder})
+        endforeach()
+    endforeach()
+endforeach()
 
+# Global target
 add_custom_target("dorie" DEPENDS richards transport)
 
 # enable setting operator scheme from config file

dune/dorie/common/CMakeLists.txt

@@ -11,7 +11,6 @@ install(FILES
     h5tools.hh
     interpolator.hh
     setup_inifile.hh
-    simulation_base.hh
     time_controller.hh
     typedefs.hh
     util.hh

dune/dorie/common/boundary_condition.hh

@@ -95,8 +95,8 @@ namespace Dorie{
 		const DF height = extensions[dim-1]; 	//!< Domain height. This must be set to the maximum height of the domain!
 		const DF depth 	= extensions[1]; 		//!< Domain depth. depth=height for dim=2
 		const std::string bcFilePath; 	//!< Path to file containing BC data
-		const RF tStart; 	//!< Starting time of simulation
-		const RF tEnd; 		//!< Finish time of simulation
+		const RF tStart; 	//!< Starting time of model
+		const RF tEnd; 		//!< Finish time of model
 
 		//! Boolean whether consecutive BC values of the same type will be interpolated.
 		const bool interpolate;

dune/dorie/common/finite_element/raviart_thomas_volume/local_basis.hh

@@ -11,6 +11,8 @@
 #include <dune/common/power.hh>
 #include <dune/common/typetraits.hh>
 
+#include <dune/pdelab/finiteelementmap/qkdg.hh>
+
 #include <vector>
 
 namespace Dune{

dune/dorie/common/finite_element/skeleton_fem.hh

@@ -8,6 +8,9 @@
 
 #include <dune/common/power.hh>
 
+#include <dune/pdelab/finiteelement/l2orthonormal.hh>
+#include <dune/pdelab/finiteelementmap/finiteelementmap.hh>
+
 namespace Dune{
 namespace Dorie{
 
@@ -271,4 +274,4 @@ struct SkeletonFiniteElementMap<DF,RF,dim,k,Dune::GeometryType::cube>
 } // namespace Dorie
 } // namespace Dune
 
-#endif // DUNE_DORIE_SKELETON_FEM_HH
\ No newline at end of file
+#endif // DUNE_DORIE_SKELETON_FEM_HH

dune/dorie/common/flux_reconstruction/raviart_thomas.hh

 #ifndef DUNE_DORIE_RAVIART_THOMAS_PROJECTION_HH
 #define DUNE_DORIE_RAVIART_THOMAS_PROJECTION_HH
 
+// hard-coded bool helpers
+#define DORIE_SUPPORT_RT_SIMPLEX(dim, order) (order <= 2)
+#define DORIE_SUPPORT_RT_CUBE(dim, order) (dim==2) ? (order <= 2) : (order <= 1)
+
 #include <vector>
 #include <string>
 
 #include <dune/common/exceptions.hh>
+#include <dune/common/parametertree.hh>
+
+#include <dune/pdelab/backend/istl.hh>
+#include <dune/pdelab/gridoperator/gridoperator.hh>
 
 #include <dune/dorie/common/logging.hh>
+#include <dune/dorie/common/utility.hh>
 
 #include <dune/dorie/common/flux_reconstruction/raviart_thomas/assembler.hh>
 #include <dune/dorie/common/flux_reconstruction/raviart_thomas/local_engine.hh>
@@ -26,28 +35,30 @@ namespace Dorie{
  *             reconstruction method is available for the combination of the
  *             used template parameters.
  *
- * @tparam     GV     Grid view
+ * @tparam     dim    Grid dimension
  * @tparam     order  Order of the flux reconstruction.
  * @tparam     gt     Geometry type.
  */
-template<class GV, unsigned int order, Dune::GeometryType::BasicType gt>
+template<int dim, unsigned int order, Dune::GeometryType::BasicType gt>
 struct RaviartThomasFluxReconstructionHelper
 {
 private:
-    static constexpr int dim = GV::dimension;
     static_assert(dim==2||dim==3);
     static_assert(gt==GeometryType::simplex||gt==GeometryType::cube);
     // hard-coded bool helpers
-    static constexpr bool val_2d_simplex = true;
-    static constexpr bool val_3d_simplex = true;
-    static constexpr bool val_2d_cube = (order <= 2);
-    static constexpr bool val_3d_cube = (order <= 1);
-    static constexpr bool val_simplex = (dim==2) ? val_2d_simplex : val_3d_simplex;
-    static constexpr bool val_cube = (dim==2) ? val_2d_cube : val_3d_cube;
+    static constexpr bool val_simplex = DORIE_SUPPORT_RT_SIMPLEX(dim, order);
+    static constexpr bool val_cube = DORIE_SUPPORT_RT_CUBE(dim, order);
 public:
     static constexpr bool enable = (gt==GeometryType::simplex) ? val_simplex : val_cube;
 };
 
+/// Shortcut helper for querying if flux reconstruction is available
+/** \see RaviartThomasFluxReconstructionHelper
+ */
+template<int dim, unsigned int rt_order, Dune::GeometryType::BasicType gt>
+constexpr bool supports_flux_reconstr_v
+    = RaviartThomasFluxReconstructionHelper<dim, rt_order, gt>::enable;
+
 /*-------------------------------------------------------------------------*//**
  * @brief      Raviart Thomas flux reconstruction for discontinuous Galerkin
  *             grid operators.

dune/dorie/common/grid_function_writer.hh

@@ -77,8 +77,8 @@ public:
   }
 
 private:
-  const Entity* _entity;
   std::shared_ptr<const GF> _gf;
+  const Entity* _entity;
 };
 
 

dune/dorie/common/modules.dox

@@ -238,8 +238,6 @@
 
 @}
 
-@defgroup Models Models
-
 @defgroup LocalOperators Local Operators
 @{
   Local operators are in many senses the heart of dorie; in them, we transform

dune/dorie/common/setup.hh

@@ -118,7 +118,7 @@ namespace Setup
     }
 
     /*------------------------------------------------------------------------*//**
-     * @brief      Set up the configuration keys for Richards simulations
+     * @brief      Set up the configuration keys for Richards models
      *
      * @param      ini   The inifile
      */
@@ -143,7 +143,7 @@ namespace Setup
     }
 
     /*------------------------------------------------------------------------*//**
-     * @brief      Set up the configuration keys for Transport simulations
+     * @brief      Set up the configuration keys for Transport models
      *
      * @param      ini   The inifile
      */

dune/dorie/common/time_controller.hh

@@ -29,8 +29,8 @@ private:
 	const R dtmax, dtmin; 	//!< time step limits
 	const R eps; 			//!< error margin
 	const R dtinc, dtdec; 	//!< time step mutliplicators
-	const R tBegin; 		//!< simulation time limits
-	R tEnd; 				//!< simulation time limits
+	const R tBegin; 		//!< model time limits
+	R tEnd; 				//!< model time limits
 	const int itmax, itmin; //!< newton iteration limits
 
 	const TSC& tsc; 		//!< Class with Function getNextTimeStamp()
@@ -126,7 +126,7 @@ public:
 			// time has advanced after calculation
 			time += dt;
 
-			if(time >= tEnd-eps) // Simulation has ended. Do nothing
+			if(time >= tEnd-eps) // Model has ended. Do nothing
 				return true;
 
 			dt = std::max(dt,dtmin);
@@ -142,7 +142,7 @@ public:
 			if(changeTime < 0.0 && time+dt > tEnd){
 				// time step adjustment to tEnd
 				dt = tEnd-time;
-				_log->trace("Adjusting time step to simulation end at: {:.2e}",
+				_log->trace("Adjusting time step to model end at: {:.2e}",
 							tEnd);
 			}
 			else if(changeTime > 0.0 && time+dt >= changeTime){

dune/dorie/common/util.hh

@@ -21,7 +21,7 @@ namespace Dorie{
 
 /**
  * @brief      Enum class for output policy.
- * @details    It defines when a simulation class should produce an output.
+ * @details    It defines when a model class should produce an output.
  */
 enum class OutputPolicy {None,EndOfRichardsStep,EndOfTransportStep};
 

dune/dorie/common/utility.hh

@@ -8,6 +8,11 @@
 #include <memory>
 #include <utility>
 
+#include <sys/types.h>
+#include <sys/stat.h>
+#include <cstdio>
+#include <cerrno>
+
 #include <yaml-cpp/yaml.h>
 
 #include <dune/common/exceptions.hh>
@@ -116,6 +121,30 @@ inline bool is_none (const std::string& in)
     return false;